BedGraph file in IGV

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Hersh Parikh

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Oct 21, 2012, 11:44:22 PM10/21/12
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Hi

I was trying to load bedgraph file in IGV but its not allowing me to do so. I have got the output in bedgraph format from one of the peak calling algorithm MACS. Can anyone please help in this?

Regards
Hersh

Jim Robinson

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Oct 22, 2012, 11:51:20 PM10/22/12
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I will try to help you but you'll have to describe the problem first.   What exactly is happening?  Does the filename have the proper extension  (.bedgraph)?  

Jim

Hersh Parikh

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Oct 23, 2012, 2:33:05 AM10/23/12
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Hi Jim,

Sorry for not posting the exact error message.

Error message is: cannot determine file type of :sample.bdg 
is this a sample information file?


Regards
Hersh

James Robinson

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Oct 23, 2012, 8:47:12 AM10/23/12
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OK, the extension has to be ".bedgraph",   note  ".bdg".

Jim


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Giulio Genovese

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Nov 27, 2012, 12:16:46 PM11/27/12
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It would be nice if this information was visualized in the http://www.broadinstitute.org/software/igv/bedgraph link, as I had the exact same problem.

Jacob Silterra

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Nov 27, 2012, 12:53:00 PM11/27/12
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Agreed; taken care of


On Tue, Nov 27, 2012 at 12:16 PM, Giulio Genovese <giulio....@gmail.com> wrote:
It would be nice if this information was visualized in the http://www.broadinstitute.org/software/igv/bedgraph link, as I had the exact same problem.

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Jacob Silterra
Software Engineer
Broad Institute

Ginger Jiang

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Jun 12, 2015, 5:25:48 AM6/12/15
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it would be easier to manually change ".bdg"in the file name to ".bedgraph". IGV would open the bedgraph file without error~

在 2012年10月23日星期二 UTC+8下午2:33:05，Hersh Parikh写道：

Jim Robinson

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Jun 12, 2015, 10:38:00 AM6/12/15
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Yes, thats correct, we rely on extensions.   Upwards of 40 file formats are supported and without an extension there is often no way to determine the format.
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